Ancient DNA analysis affirms the canid from Altai as a primitive dog

Abstract

The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication.

Figure 1. Map depicting the geographic origin of the Altai dog specimen.

Figure 2. Consensus Neighbour Joining tree (1,000 bootstrap steps) built assuming the Tamura-Nei substitution model, the best fit model for the dataset comprising complete mitochondrial genomes from coyotes (Coyotes), wolves (OWW, NWW – Old and New World wolves, respectively) and dogs combined with partial control region sequences from the Altai specimen (Altai dog) and additional prehistoric canids (pre-Columbian dogs, eastern Beringian wolves).

We highlighted all clades containing modern dogs in light blue and enlarged Clade A for better visibility. The position of the Altai specimen is marked with a light blue arrow in the enlargement. Bootstrap values are shown with an asterisk whenever larger than 50.

Figure 3. Likelihood mapping analysis off all 142 canid sequences clustered into four groups.

Upper panel shows the distribution pattern of all quartets and the lower panel depicts the fraction of each occupied region. Quartets situated in the centre part of the triangle support a star-shaped sequence evolution whereas quartets in the three corners support resolved topologies, respectively. A) Likelihood mapping pattern when clustering the sequences into Altai dog, dogs, wolves and coyotes. B) Likelihood mapping pattern when sequences were clustered as follows: Altai dog, dogs, wolves and prehistoric New World canids taken from –.

Figure 4. Box plot showing the genetic differences between the Altai specimen and various groupings of contemporary and extinct canids.

Genetic distances were estimated under the assumption of Kimura 2 Parameter substitution model, the best fit for the truncated alignment of canids. The highlighted box shows the minimum and maximum counted differences. ¹ Leonard et al. 2007 ; ² Leonard et al. 2002 .